Computes principal components from a numeric matrix or data frame with automatic scaling and zero-variance removal. Returns all principal components as a data frame. Wrapper for stats::prcomp().
Value
Data frame where each column is a principal component, ordered by decreasing variance explained. Columns are named with the pattern <prefix>_<number> (e.g., "pca_factor_1", "pca_factor_2"). The number of rows matches the number of rows in x.
Details
This function performs Principal Component Analysis (PCA) to create uncorrelated linear combinations of the original variables. The PCA process:
Removes columns with zero variance (constant values)
Scales all remaining variables to mean = 0 and standard deviation = 1
Computes principal components using singular value decomposition
Returns all principal components ordered by decreasing variance explained
Usage in spatial analysis:
PCA is useful for dimension reduction when working with spatial distance matrices or multiple correlated spatial predictors. It creates orthogonal (uncorrelated) variables that capture the main patterns of variation while reducing dimensionality.
For spatial modeling with rf_spatial(), principal components of distance matrices can serve as alternative spatial predictors to Moran's Eigenvector Maps (MEMs). Use pca_multithreshold() to compute PCA across multiple distance thresholds for multi-scale spatial modeling.
See also
pca_multithreshold(), mem(), stats::prcomp()
Other spatial_analysis:
filter_spatial_predictors(),
mem(),
mem_multithreshold(),
moran(),
moran_multithreshold(),
pca_multithreshold(),
rank_spatial_predictors(),
residuals_diagnostics(),
residuals_test(),
select_spatial_predictors_recursive(),
select_spatial_predictors_sequential()
Examples
data(plants_distance)
# Compute principal components from distance matrix
pca_components <- pca(x = plants_distance)
# View structure
head(pca_components)
#> pca_factor_1 pca_factor_2 pca_factor_3 pca_factor_4 pca_factor_5 pca_factor_6
#> 1 -12.218870 -4.7269136 -1.02356852 -1.41670978 1.0808699 -0.17113394
#> 2 -0.152152 -13.4390215 1.43470475 -0.63694341 1.0094228 -0.22572477
#> 3 14.991288 7.9275139 0.17176343 -0.97212017 0.9661209 0.04060681
#> 4 -8.381081 -7.3480897 -0.09181525 -2.18358185 -0.3016224 0.85599614
#> 5 -15.843009 0.3731175 -1.17424167 -0.07115725 1.5862881 -0.01073622
#> 6 -15.021061 -0.2472622 -0.65021720 -0.68574566 1.1077198 0.12448525
#> pca_factor_7 pca_factor_8 pca_factor_9 pca_factor_10 pca_factor_11
#> 1 0.16389264 -0.1854939 0.36970506 0.04912189 -0.07018169
#> 2 0.89198638 0.1585257 -0.23432374 0.06496525 0.53255119
#> 3 0.04717233 0.3787097 -0.25574073 -0.08391090 -0.16598691
#> 4 -0.47607345 -0.1259408 0.03617367 -0.45108330 0.10613139
#> 5 0.64343730 -0.2253146 0.29407574 0.42192302 -0.30848245
#> 6 0.31238846 -0.4486079 0.63329782 0.27870646 -0.52757233
#> pca_factor_12 pca_factor_13 pca_factor_14 pca_factor_15 pca_factor_16
#> 1 0.05178803 0.30409248 -0.13361100 0.12942465 0.1225077765
#> 2 -0.27520790 0.25148325 0.15005233 -0.13795618 -0.1249840289
#> 3 0.20496582 0.04401895 0.11332852 0.13199024 -0.1647649389
#> 4 -0.09394757 -0.18780889 0.16612673 -0.03015461 0.0002037343
#> 5 0.19246910 -0.38299782 0.09823305 -0.14191585 0.0602109577
#> 6 0.21989515 -0.19771265 -0.03633891 -0.06837262 0.0271914263
#> pca_factor_17 pca_factor_18 pca_factor_19 pca_factor_20 pca_factor_21
#> 1 -0.12383546 -0.03213864 -0.106260319 0.06712701 -0.08753545
#> 2 -0.15189266 0.38563779 -0.159559082 -0.11919273 -0.08374455
#> 3 -0.01552011 -0.03148090 -0.008176379 -0.02818273 -0.04948034
#> 4 -0.07020498 -0.01520840 -0.043250164 0.02549078 -0.04066914
#> 5 0.02617577 -0.04135578 0.026607549 -0.02478234 0.03146661
#> 6 0.05915808 -0.01277080 -0.017757284 0.05346382 0.01173331
#> pca_factor_22 pca_factor_23 pca_factor_24 pca_factor_25 pca_factor_26
#> 1 -0.12257589 0.011928130 0.047196344 -0.096755377 0.027237569
#> 2 0.38572581 0.291686864 -0.062073152 -0.120383766 -0.056748354
#> 3 -0.04171398 0.064831667 -0.071633868 -0.008804744 0.003971765
#> 4 -0.08864117 -0.008214126 -0.046787052 -0.031373813 0.006599218
#> 5 0.04682520 0.100408094 -0.001627967 0.035774906 0.035893769
#> 6 0.01861755 0.082514677 -0.019536828 0.003531422 0.008376026
#> pca_factor_27 pca_factor_28 pca_factor_29 pca_factor_30 pca_factor_31
#> 1 0.01639773 0.023620870 0.01474589 0.05385999 0.006066492
#> 2 -0.05365591 0.059149981 -0.05825053 -0.09315659 -0.055988415
#> 3 -0.01957043 -0.083846835 0.04520615 -0.03239597 -0.011344738
#> 4 0.01118360 0.089536885 -0.00766279 -0.06431346 -0.055689488
#> 5 -0.11336476 0.038534980 0.01537265 0.03367446 0.028330646
#> 6 -0.10979120 0.001052497 -0.01771371 0.05483260 0.004791121
#> pca_factor_32 pca_factor_33 pca_factor_34 pca_factor_35 pca_factor_36
#> 1 -0.01666689 0.014173625 0.053770918 0.00205025 -0.05091623
#> 2 -0.02998587 -0.008098609 -0.105371303 -0.05700442 -0.06777599
#> 3 -0.02185682 0.029604013 0.031289526 0.02222520 0.01147305
#> 4 0.03121135 0.008820192 -0.002248140 -0.01344441 -0.01152207
#> 5 -0.01941801 0.020031724 -0.021909535 -0.03013976 0.12869961
#> 6 -0.01447872 0.065815153 -0.006038134 0.04654905 0.02953678
#> pca_factor_37 pca_factor_38 pca_factor_39 pca_factor_40 pca_factor_41
#> 1 0.01518882 0.004170665 -0.007862882 6.116284e-02 -0.048376186
#> 2 0.03637844 0.057685574 -0.014663405 9.788886e-02 0.032312711
#> 3 -0.01888614 -0.025302688 -0.025660515 2.108422e-03 0.006477309
#> 4 0.02197379 0.008230668 -0.001942349 8.419748e-05 0.007906684
#> 5 -0.06644903 -0.007705879 0.099842748 2.979452e-02 0.043818191
#> 6 -0.04360430 0.004363007 0.050607841 -1.043521e-02 0.027795196
#> pca_factor_42 pca_factor_43 pca_factor_44 pca_factor_45 pca_factor_46
#> 1 0.02414571 -2.415681e-02 0.001800041 0.026411293 0.006666762
#> 2 -0.07913444 1.858623e-02 -0.067415167 0.004157492 -0.025865261
#> 3 0.01346260 1.125391e-03 -0.001190597 0.007412055 -0.007767644
#> 4 0.03467140 -2.440812e-05 0.007102014 0.013754655 -0.001743820
#> 5 -0.05668840 2.461044e-02 0.016781004 0.023126166 -0.007705036
#> 6 -0.05851598 3.580723e-03 0.008754991 0.014698688 -0.030865475
#> pca_factor_47 pca_factor_48 pca_factor_49 pca_factor_50 pca_factor_51
#> 1 0.020391592 -0.012664836 0.007547133 0.023034661 0.004694774
#> 2 0.015473506 0.006008116 -0.062786558 -0.014280397 -0.001677320
#> 3 0.007372088 0.004109563 -0.018279648 0.002942758 -0.005418950
#> 4 -0.031039855 0.012964398 -0.040813210 0.010362134 0.034949252
#> 5 -0.045129219 -0.004286254 -0.015247223 -0.015841910 0.001048509
#> 6 0.001132289 -0.012956455 0.025602739 -0.018664475 -0.022976740
#> pca_factor_52 pca_factor_53 pca_factor_54 pca_factor_55 pca_factor_56
#> 1 -0.025404842 0.032623154 -0.047267023 -0.013893384 0.0021070271
#> 2 -0.004607569 -0.012838075 -0.001821838 -0.025254284 0.0114679627
#> 3 0.009159499 0.001666848 -0.008190814 0.001660283 -0.0121129480
#> 4 0.008066760 -0.008190933 0.011121698 -0.007222848 0.0091388355
#> 5 0.030180445 -0.013321524 0.053224623 -0.001933732 -0.0211298838
#> 6 0.020276103 -0.001399503 0.027929512 -0.032430372 -0.0003394445
#> pca_factor_57 pca_factor_58 pca_factor_59 pca_factor_60 pca_factor_61
#> 1 0.014561226 0.009854423 1.517351e-02 0.005028425 0.003765274
#> 2 0.006463985 -0.008660429 1.974217e-02 -0.019711735 -0.011243243
#> 3 0.005779770 -0.010317505 -4.624960e-03 0.003595268 0.025708569
#> 4 0.015586881 0.003939412 2.650690e-02 -0.013708872 -0.006008721
#> 5 0.008179781 0.007463324 5.716711e-05 0.013009104 0.013781442
#> 6 -0.001738920 0.007649249 5.650609e-03 -0.053586468 -0.013306561
#> pca_factor_62 pca_factor_63 pca_factor_64 pca_factor_65 pca_factor_66
#> 1 -0.01443245 -0.020903560 -0.003100600 0.005844552 0.0372366495
#> 2 0.01312585 -0.020454026 0.001098523 0.010238331 0.0159911593
#> 3 0.01258284 0.002276682 0.003880994 0.023998878 -0.0055508723
#> 4 -0.01209324 0.020644614 0.002414000 0.018382731 0.0001990194
#> 5 0.01003047 0.053279489 0.036158294 0.003670798 0.0381195134
#> 6 -0.01067314 0.030331278 -0.017597927 0.029716297 0.0426275504
#> pca_factor_67 pca_factor_68 pca_factor_69 pca_factor_70 pca_factor_71
#> 1 0.0010503122 0.0139659584 0.026727815 -0.020961170 9.846052e-03
#> 2 -0.0008296579 0.0072093550 -0.040881516 -0.005658544 6.925288e-03
#> 3 -0.0309960594 -0.0058447358 -0.003605370 -0.006899793 1.556355e-02
#> 4 -0.0016614774 0.0009117931 0.021929053 0.002776474 -3.526866e-03
#> 5 -0.0025993536 0.0058254436 0.002066175 -0.010709911 -5.652187e-03
#> 6 -0.0170756697 -0.0048286562 -0.015914829 0.012081944 -5.332263e-05
#> pca_factor_72 pca_factor_73 pca_factor_74 pca_factor_75 pca_factor_76
#> 1 -0.001418242 0.022445397 0.0010801764 0.003191195 0.001078183
#> 2 0.004784309 -0.015150473 -0.0002797033 -0.007967606 0.005288832
#> 3 -0.001341904 -0.014542230 -0.0008825448 0.002968047 -0.004191831
#> 4 0.008830803 -0.003138701 -0.0008636915 0.016688462 -0.009319554
#> 5 0.024672770 0.016548767 -0.0036338664 0.011119600 -0.014432798
#> 6 0.006065151 -0.011891668 0.0313931906 0.010340800 0.008442226
#> pca_factor_77 pca_factor_78 pca_factor_79 pca_factor_80 pca_factor_81
#> 1 -0.012521496 -0.007302162 0.008774992 0.020883664 -0.0073685913
#> 2 0.001030807 -0.009184283 0.003802436 -0.007616421 -0.0129572315
#> 3 -0.024462263 -0.008914295 -0.019288148 -0.012522002 0.0251701790
#> 4 0.006272017 -0.003077019 -0.007887029 0.006704440 0.0002261765
#> 5 0.013131693 -0.008885067 -0.010856820 0.013357000 0.0143584439
#> 6 -0.025507250 0.019942347 0.006489815 0.008988333 -0.0251653261
#> pca_factor_82 pca_factor_83 pca_factor_84 pca_factor_85 pca_factor_86
#> 1 -0.001202835 -1.477227e-03 0.009039324 -0.0007291578 0.035824582
#> 2 0.001422500 -1.622130e-03 0.011734625 0.0045787163 -0.004299872
#> 3 0.013249140 -5.817333e-05 0.007009282 0.0155778584 0.015109644
#> 4 0.001032491 -3.848187e-03 0.001262538 -0.0091486735 0.003927683
#> 5 -0.009258615 -3.353159e-02 -0.006905636 0.0021574034 -0.005526659
#> 6 -0.024892042 3.145947e-02 -0.013766533 0.0309063905 -0.004873954
#> pca_factor_87 pca_factor_88 pca_factor_89 pca_factor_90 pca_factor_91
#> 1 0.002623626 -0.0123973717 0.007813104 0.0031385132 -0.0080520562
#> 2 0.003409765 -0.0062451913 -0.006278396 -0.0101431427 0.0006174194
#> 3 -0.008943485 0.0071503020 -0.002834640 -0.0165990766 -0.0175161450
#> 4 -0.006964844 -0.0004994315 -0.001609755 0.0002335438 -0.0087661751
#> 5 0.005690156 0.0029768229 0.001099237 -0.0082309927 0.0016073007
#> 6 0.002082131 0.0030015916 -0.007491569 0.0011363243 -0.0103309665
#> pca_factor_92 pca_factor_93 pca_factor_94 pca_factor_95 pca_factor_96
#> 1 -0.002022747 0.008180433 0.0009921981 -0.001990799 -0.004699202
#> 2 0.004219358 -0.002354508 0.0012505203 0.008259348 -0.003736354
#> 3 0.007080646 0.003834253 0.0076667112 0.001663238 -0.008994829
#> 4 0.004826356 -0.013043856 0.0068045528 0.001349340 0.007483395
#> 5 -0.018659699 -0.014271602 -0.0030404569 -0.014551666 -0.004728918
#> 6 0.013643661 0.008770535 0.0071755333 -0.003756933 0.013150254
#> pca_factor_97 pca_factor_98 pca_factor_99 pca_factor_100 pca_factor_101
#> 1 -0.002207605 0.007427165 -0.005044416 0.006036761 0.0082354908
#> 2 0.002575995 -0.004304952 -0.010328600 -0.001063976 0.0088247401
#> 3 0.010996662 0.001440381 0.011329838 0.002417251 -0.0074373431
#> 4 -0.001174492 0.007294115 -0.002190794 -0.001413402 0.0007128313
#> 5 0.007340681 -0.004343021 -0.014665833 -0.002971143 0.0158422924
#> 6 -0.003227112 0.013250685 0.013325597 0.005804668 -0.0074449670
#> pca_factor_102 pca_factor_103 pca_factor_104 pca_factor_105 pca_factor_106
#> 1 -2.107486e-03 -0.0050538102 -1.072138e-02 0.005042449 -0.014146967
#> 2 -4.163104e-03 -0.0081128274 -3.188264e-03 0.006097497 0.004620229
#> 3 9.173034e-03 -0.0003648861 1.668936e-03 -0.005845630 -0.010974617
#> 4 4.000354e-05 -0.0105854670 1.987363e-03 -0.005965043 0.012416825
#> 5 -7.164625e-03 0.0109963019 3.702241e-04 -0.014501543 -0.006496020
#> 6 2.372550e-03 -0.0039290496 -9.118187e-05 0.006082399 0.005452834
#> pca_factor_107 pca_factor_108 pca_factor_109 pca_factor_110 pca_factor_111
#> 1 -0.005471005 0.016500039 0.002819663 -0.004653123 0.007708291
#> 2 -0.001158567 -0.002712819 0.005831634 -0.002271941 -0.002956263
#> 3 0.006500466 -0.010372792 0.004854102 0.004183637 -0.003331111
#> 4 0.001246911 -0.001112765 -0.003532106 0.002834732 0.003439019
#> 5 0.006237827 -0.006097835 0.005211429 0.003993471 -0.002570962
#> 6 -0.004873347 -0.003701362 -0.010558482 -0.007150309 -0.001524438
#> pca_factor_112 pca_factor_113 pca_factor_114 pca_factor_115 pca_factor_116
#> 1 -0.003952538 0.0045653013 -0.0013368515 -0.009933483 -0.002714634
#> 2 -0.001076943 0.0027818844 -0.0061499239 -0.002494727 0.003586033
#> 3 0.003073674 -0.0130229097 0.0047560469 -0.008198527 -0.011500763
#> 4 -0.002896339 0.0028650230 0.0006763963 0.007636456 0.001769706
#> 5 0.001221455 -0.0004549904 0.0014539277 0.003080591 -0.002072529
#> 6 -0.002381293 0.0054539986 0.0032453504 0.004771453 -0.005019623
#> pca_factor_117 pca_factor_118 pca_factor_119 pca_factor_120 pca_factor_121
#> 1 -0.0048638037 0.005633477 0.002887800 -0.002514615 -0.0005708920
#> 2 0.0018565909 -0.004692799 -0.002562638 -0.006899320 -0.0002697497
#> 3 0.0052900072 0.002223350 -0.003077105 -0.004512190 -0.0139350131
#> 4 -0.0006496882 -0.005227474 -0.003207940 -0.003237909 -0.0046655678
#> 5 -0.0004255358 0.007940143 0.008526445 -0.002574041 0.0012491155
#> 6 0.0038133799 -0.020403018 0.010315624 -0.004139521 -0.0015877516
#> pca_factor_122 pca_factor_123 pca_factor_124 pca_factor_125 pca_factor_126
#> 1 -0.0106560804 -0.001083814 -0.0006658968 0.0073423336 -0.0070284048
#> 2 0.0090077070 0.007504832 -0.0058591945 0.0065141550 0.0028018753
#> 3 -0.0009682785 0.005523182 0.0004579705 -0.0003413708 -0.0004328339
#> 4 0.0023858712 0.003268629 -0.0047574459 -0.0049905913 0.0008219821
#> 5 0.0038843293 0.003041800 0.0047519141 0.0016705987 0.0023928933
#> 6 -0.0061776049 -0.002055496 -0.0063598483 0.0020390889 -0.0014333374
#> pca_factor_127 pca_factor_128 pca_factor_129 pca_factor_130 pca_factor_131
#> 1 -0.006286590 0.016174589 0.001263223 0.008809369 0.0007844217
#> 2 -0.003755646 0.006118608 -0.000333471 -0.001428667 -0.0003875330
#> 3 -0.003471960 0.001955072 0.001062547 -0.002427888 -0.0063628081
#> 4 -0.006542377 0.005427534 -0.003408501 -0.006111476 -0.0051645033
#> 5 0.002447952 0.002222958 0.008526361 -0.001339866 0.0015327616
#> 6 -0.003451971 -0.004414827 -0.003153497 0.004049347 0.0031799016
#> pca_factor_132 pca_factor_133 pca_factor_134 pca_factor_135 pca_factor_136
#> 1 0.001576077 -0.0034551765 -0.0016657001 4.235605e-03 0.008965261
#> 2 -0.001065540 -0.0003707375 0.0022459949 2.297459e-03 0.001292492
#> 3 -0.007801417 0.0027114636 0.0051502890 1.812157e-05 0.002718458
#> 4 0.006717089 -0.0048827438 -0.0008220446 3.319292e-03 0.001344942
#> 5 -0.004119721 0.0111216323 -0.0024121396 5.825822e-03 -0.010722194
#> 6 0.002333457 -0.0123369964 0.0046266219 -5.593454e-03 0.007505895
#> pca_factor_137 pca_factor_138 pca_factor_139 pca_factor_140 pca_factor_141
#> 1 -0.0050174834 -0.0049145326 0.0052181089 0.0037450937 0.0018008830
#> 2 0.0027541936 -0.0020220580 0.0001777766 -0.0028097672 0.0004154273
#> 3 0.0017758784 -0.0017366888 0.0007258666 0.0021162688 -0.0020838251
#> 4 0.0008824992 0.0031573241 0.0147796632 0.0044294661 -0.0053003133
#> 5 -0.0029217340 -0.0043675767 0.0031881992 0.0007351542 0.0015886475
#> 6 0.0012509244 0.0003366084 0.0029239129 0.0063622750 -0.0020722198
#> pca_factor_142 pca_factor_143 pca_factor_144 pca_factor_145 pca_factor_146
#> 1 -0.0026068052 -0.0003367131 0.0027560817 -5.609625e-03 -0.005657261
#> 2 0.0002487879 0.0002573428 0.0003372641 1.020283e-03 -0.001457623
#> 3 -0.0013652015 0.0016169310 -0.0029800277 5.104458e-04 0.001293403
#> 4 -0.0031151632 0.0043957575 0.0018912704 8.590023e-05 -0.003652177
#> 5 -0.0048742327 0.0013276455 0.0023118376 -7.673561e-03 -0.003517187
#> 6 0.0046531577 -0.0026683218 0.0016499905 6.830237e-03 0.004775202
#> pca_factor_147 pca_factor_148 pca_factor_149 pca_factor_150 pca_factor_151
#> 1 -0.0061029252 -0.0035565421 -0.001861340 -0.008083194 -0.0056149283
#> 2 -0.0009052284 -0.0009370455 -0.002669167 0.001377960 -0.0001578843
#> 3 -0.0023517305 -0.0039201739 -0.009911183 0.004120998 0.0036834729
#> 4 0.0039715343 0.0001665660 -0.001983291 -0.008294129 -0.0001393251
#> 5 -0.0006465503 -0.0005796533 0.002499816 -0.001717640 0.0006800697
#> 6 -0.0002975743 0.0044699288 -0.002798820 -0.002339263 0.0034729164
#> pca_factor_152 pca_factor_153 pca_factor_154 pca_factor_155 pca_factor_156
#> 1 0.0045631129 -0.0046219840 2.334998e-03 3.047554e-04 -0.0048538663
#> 2 0.0034566581 0.0020441129 -4.943131e-05 -1.807490e-03 0.0001944009
#> 3 -0.0056633589 -0.0046648255 -2.059394e-03 2.622015e-03 0.0008236737
#> 4 0.0040573301 0.0009158379 2.126340e-06 -8.965051e-04 0.0051164715
#> 5 0.0005837352 -0.0040328712 1.406840e-03 1.053436e-05 -0.0019852042
#> 6 0.0001760928 -0.0023989761 -1.745994e-03 -6.470187e-04 0.0007113196
#> pca_factor_157 pca_factor_158 pca_factor_159 pca_factor_160 pca_factor_161
#> 1 -0.002376922 -0.0006463849 0.0016271490 -0.0047427594 0.0021606392
#> 2 -0.001205179 0.0019376167 -0.0006414849 0.0002928884 -0.0008929483
#> 3 -0.001426107 -0.0010957451 -0.0013246046 0.0006462936 -0.0016409490
#> 4 0.003205802 -0.0021449047 -0.0019383454 -0.0001931808 -0.0001845291
#> 5 -0.001309246 -0.0001770396 -0.0014746283 -0.0007331362 0.0010905307
#> 6 -0.004014299 0.0002532625 -0.0011327084 -0.0059362286 -0.0011292474
#> pca_factor_162 pca_factor_163 pca_factor_164 pca_factor_165 pca_factor_166
#> 1 -1.625107e-05 -0.0036304029 -0.0006836676 -3.821733e-03 -0.0003690380
#> 2 5.072323e-04 -0.0001302898 0.0003842730 -4.834914e-05 0.0001040518
#> 3 7.725987e-03 0.0044199226 0.0008145663 -3.135122e-03 -0.0012500786
#> 4 2.265563e-03 -0.0020041074 0.0023424750 1.096546e-03 -0.0043874580
#> 5 -5.241624e-04 -0.0005648413 0.0008161844 -1.878067e-03 -0.0014712651
#> 6 9.556222e-04 0.0027865343 -0.0010835173 6.369167e-03 0.0017727031
#> pca_factor_167 pca_factor_168 pca_factor_169 pca_factor_170 pca_factor_171
#> 1 -0.0020168803 0.0010270895 2.293481e-03 0.0037682948 -9.269175e-04
#> 2 -0.0004194485 -0.0008282748 1.014649e-03 0.0016243577 8.646181e-04
#> 3 0.0010642525 -0.0029866373 6.631094e-03 0.0013163323 -7.083477e-05
#> 4 -0.0003694773 -0.0025460982 2.348497e-03 -0.0016638792 -1.823382e-03
#> 5 0.0005498941 0.0005097873 -3.754092e-05 0.0030116098 1.084386e-03
#> 6 0.0018600546 0.0010724609 -3.440681e-04 -0.0001871951 5.057628e-04
#> pca_factor_172 pca_factor_173 pca_factor_174 pca_factor_175 pca_factor_176
#> 1 0.0010741327 7.869634e-05 -0.0018137291 0.0016818528 0.0034921669
#> 2 -0.0009106406 -1.199207e-03 -0.0009630829 -0.0004162441 0.0009601207
#> 3 0.0014229045 -6.041572e-04 0.0017283507 -0.0022130900 0.0018524454
#> 4 -0.0004757255 1.623497e-03 -0.0020098359 -0.0019315081 -0.0045234135
#> 5 0.0024646662 -1.573010e-03 0.0011487263 0.0026956591 0.0009415840
#> 6 0.0002855238 -9.799013e-04 -0.0021798443 -0.0018322023 -0.0014250661
#> pca_factor_177 pca_factor_178 pca_factor_179 pca_factor_180 pca_factor_181
#> 1 -6.435065e-04 0.0014073139 -0.0015892628 0.0027984126 -0.0001873233
#> 2 -5.217270e-04 0.0003228545 -0.0006264088 -0.0009585276 0.0007842583
#> 3 5.546655e-04 -0.0012807971 -0.0006990916 0.0003243599 -0.0025486156
#> 4 2.236366e-03 -0.0049406512 0.0081873788 -0.0017668225 0.0043978659
#> 5 9.270613e-05 0.0001465795 0.0014806924 -0.0015435663 0.0004369851
#> 6 -2.259221e-03 0.0006596395 0.0005891348 0.0013571753 -0.0016411605
#> pca_factor_182 pca_factor_183 pca_factor_184 pca_factor_185 pca_factor_186
#> 1 1.181043e-04 0.0010111435 -5.354189e-04 -0.0002801031 -1.678680e-03
#> 2 -1.508219e-03 0.0004899232 1.063188e-03 0.0004077291 -6.841534e-04
#> 3 2.406696e-03 -0.0001202167 9.582576e-05 0.0007441460 -4.374883e-04
#> 4 4.725387e-03 0.0018939051 2.232272e-04 0.0006954618 1.275139e-03
#> 5 7.087573e-05 -0.0001083608 4.272991e-04 -0.0004710478 -5.361893e-04
#> 6 1.027883e-03 -0.0002235611 5.703856e-04 -0.0007172799 -9.501729e-05
#> pca_factor_187 pca_factor_188 pca_factor_189 pca_factor_190 pca_factor_191
#> 1 -7.166260e-05 -4.189923e-04 -3.088609e-03 0.0004835602 -2.326073e-03
#> 2 -7.545984e-05 -1.702492e-03 -5.878207e-04 -0.0004272058 -8.862991e-05
#> 3 1.047854e-03 3.067411e-04 -1.154013e-03 -0.0011069086 -1.451557e-03
#> 4 -9.659181e-04 7.661696e-04 8.988878e-05 0.0005897016 1.984714e-03
#> 5 6.788297e-04 5.759520e-06 -5.499065e-04 0.0003783056 -1.765949e-03
#> 6 -4.423718e-04 -4.118113e-04 9.820378e-05 -0.0007286169 -6.285178e-04
#> pca_factor_192 pca_factor_193 pca_factor_194 pca_factor_195 pca_factor_196
#> 1 0.0002588062 0.0003493341 0.0021549399 0.0000360850 0.0013433311
#> 2 -0.0001154636 -0.0008785079 -0.0003964951 0.0005900417 0.0001143417
#> 3 -0.0008911994 -0.0007910467 -0.0011616302 -0.0015576652 0.0009741499
#> 4 -0.0019569310 0.0024376868 -0.0008727183 -0.0014393105 -0.0023225320
#> 5 0.0007551236 0.0006117586 0.0008180071 0.0007254657 0.0014895054
#> 6 0.0012707336 -0.0002999761 0.0002411216 0.0012577197 0.0004607035
#> pca_factor_197 pca_factor_198 pca_factor_199 pca_factor_200 pca_factor_201
#> 1 0.0014671790 5.218250e-04 -0.0004677686 -0.0002086430 -1.884772e-04
#> 2 -0.0002028889 5.344590e-04 0.0001659118 0.0002371074 9.396763e-06
#> 3 -0.0009844042 3.506239e-04 0.0006754119 -0.0002426923 1.674313e-03
#> 4 0.0005511763 -4.581004e-06 0.0004301918 -0.0006559327 -5.552159e-04
#> 5 0.0012481530 7.822894e-04 -0.0010955627 0.0003812589 7.116311e-04
#> 6 0.0009865644 1.050441e-03 -0.0002663372 -0.0014076291 -1.762485e-04
#> pca_factor_202 pca_factor_203 pca_factor_204 pca_factor_205 pca_factor_206
#> 1 -4.320959e-05 5.793507e-04 -0.0007216949 -7.170136e-04 -9.487223e-04
#> 2 -3.322505e-04 -5.065128e-04 -0.0003328333 -2.455606e-04 1.598527e-04
#> 3 3.483591e-06 1.111713e-03 0.0010772546 -8.692387e-05 1.050238e-04
#> 4 -3.781564e-04 -5.325165e-06 0.0012055402 -1.656318e-03 -2.574953e-04
#> 5 -1.302707e-03 -9.734912e-04 -0.0004873443 -5.580093e-04 -9.713174e-06
#> 6 6.138046e-04 5.853623e-04 0.0003437593 4.297516e-05 2.670179e-04
#> pca_factor_207 pca_factor_208 pca_factor_209 pca_factor_210 pca_factor_211
#> 1 6.519079e-04 5.982805e-04 -3.558925e-04 -3.936119e-04 -1.007908e-04
#> 2 -4.097148e-04 -3.762327e-05 -4.657573e-05 9.417593e-05 -1.693671e-04
#> 3 -6.438704e-04 1.407048e-04 -1.010224e-03 1.754172e-04 2.187955e-04
#> 4 9.628832e-04 5.924123e-04 -3.752844e-04 -7.738198e-04 -5.900585e-04
#> 5 -1.970368e-06 7.940002e-05 -3.283343e-04 8.843315e-05 8.805113e-05
#> 6 4.198985e-04 3.504750e-04 4.303783e-04 2.228233e-04 3.017635e-04
#> pca_factor_212 pca_factor_213 pca_factor_214 pca_factor_215 pca_factor_216
#> 1 3.026472e-04 4.873313e-05 1.528232e-04 -9.627762e-05 2.557918e-04
#> 2 1.555140e-04 2.755780e-04 5.051165e-05 -2.209656e-04 1.196059e-04
#> 3 7.616931e-04 5.782473e-04 9.730206e-04 -3.269466e-04 -5.153416e-05
#> 4 1.443150e-04 -8.248354e-04 -2.803188e-04 -3.566867e-04 -2.736934e-04
#> 5 -2.394113e-04 1.790033e-04 -4.588106e-04 -5.776264e-05 -4.672789e-06
#> 6 5.109468e-05 -1.508575e-04 -1.078477e-04 4.933810e-05 2.766367e-05
#> pca_factor_217 pca_factor_218 pca_factor_219 pca_factor_220 pca_factor_221
#> 1 2.259651e-04 1.926635e-04 -1.087614e-06 9.179728e-05 6.726906e-05
#> 2 -2.683465e-05 -1.018192e-04 7.629508e-05 8.625351e-05 -4.951099e-06
#> 3 -2.427039e-04 8.433062e-04 -5.688865e-04 -3.327618e-04 -1.630345e-04
#> 4 1.649782e-04 1.112468e-04 4.228612e-05 -1.759042e-04 2.048813e-05
#> 5 5.297835e-06 -2.595331e-04 -8.156397e-05 -3.094585e-04 -3.278914e-05
#> 6 -1.862317e-04 -1.474961e-05 -1.575735e-04 1.091648e-04 1.882883e-05
#> pca_factor_222 pca_factor_223 pca_factor_224 pca_factor_225 pca_factor_226
#> 1 1.242357e-04 -2.546247e-05 -6.662277e-05 -7.914239e-05 1.849906e-05
#> 2 -4.601476e-05 -3.956917e-06 5.731406e-05 2.207807e-06 1.324344e-05
#> 3 -1.222847e-04 1.719210e-04 -3.015813e-05 4.324422e-05 -1.377595e-04
#> 4 1.186649e-04 1.094037e-04 2.310370e-05 -1.354702e-04 -1.185625e-04
#> 5 3.746402e-05 1.220189e-04 -4.447270e-05 8.816518e-06 -3.970581e-05
#> 6 -2.715193e-05 5.975994e-05 -2.321644e-05 -3.869402e-06 2.806507e-05
#> pca_factor_227
#> 1 -5.342948e-15
#> 2 -4.440892e-16
#> 3 -6.522560e-16
#> 4 4.163336e-17
#> 5 -3.747003e-16
#> 6 3.608225e-16
dim(pca_components)
#> [1] 227 227
# Check column names
colnames(pca_components)[1:5]
#> [1] "pca_factor_1" "pca_factor_2" "pca_factor_3" "pca_factor_4" "pca_factor_5"
# Custom column prefix
pca_custom <- pca(
x = plants_distance,
colnames.prefix = "distance_pc"
)
colnames(pca_custom)[1:3]
#> [1] "distance_pc_1" "distance_pc_2" "distance_pc_3"